Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6671
Trapped Gene
Trak1 (ENSMUSG00000032536)
Vector Insertion
Chr 9: 121355012 - 121355807
Public Clones HMA257 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 27% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000501964 (Chr9:121354933..121355011 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATGAGGAGAAGGAGCAGCAG Chr9:121354964..121354983 59.7 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000501964 (Chr9:121354933..121355011 +)
Downstram Exon
ENSMUSE00000499273 (Chr9:121355808..121355938 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATGAGGAGAAGGAGCAGCAG Chr9:121354964..121354983 59.7 55 TAAGTCCACGATTTGCGACA Chr9:121355923..121355942 60.26 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000633538 Chr9:121206620..121206951 CTACGCTGAGCCTCGCAGTC Chr9:121206831..121206850 63.67 65
upstream ENSMUSE00000633537 Chr9:121273119..121273417 GGAAGATGCTCCCAGCTACA Chr9:121273368..121273387 60.36 55
upstream ENSMUSE00000259358 Chr9:121276076..121276309 AAGCTTGGGAAAACTGCTGA Chr9:121276124..121276143 59.99 45
upstream ENSMUSE00000528168 Chr9:121300975..121301169 AACAGCTGCCCCATTACAAG Chr9:121301029..121301048 60.13 50
upstream ENSMUSE00000633536 Chr9:121300975..121301169 AACAGCTGCCCCATTACAAG Chr9:121301029..121301048 60.13 50
upstream ENSMUSE00000520674 Chr9:121340597..121340673 TGACATTGATGCTGTCACGA Chr9:121340640..121340659 59.82 45
upstream ENSMUSE00000220555 Chr9:121349788..121349904 GAAGAGCAGGTGGAGCACAT Chr9:121349875..121349894 60.42 55
upstream ENSMUSE00000220546 Chr9:121351810..121351910 TGAAAGACGAGCTGCTTCAA Chr9:121351838..121351857 59.86 45
upstream ENSMUSE00000497415 Chr9:121352744..121352852 TCAAGGACCTCGAAGAGGAG Chr9:121352812..121352831 59.53 55
upstream ENSMUSE00000501964 Chr9:121354933..121355011 ATGAGGAGAAGGAGCAGCAG Chr9:121354964..121354983 59.7 55

*** Putative Vector Insertion (Chr 9: 121355012 - 121355807) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000499273 Chr9:121355808..121355938 TAAGTCCACGATTTGCGACA Chr9:121355923..121355942 60.26 45
downstream ENSMUSE00000510957 Chr9:121357226..121357300 TGCTGGACAAGCTCTTCATT Chr9:121357260..121357279 58.6 45
downstream ENSMUSE00000508239 Chr9:121357940..121358071 CTCCGCGTACTTATCCTCCA Chr9:121357972..121357991 60.23 55
downstream ENSMUSE00000512812 Chr9:121360769..121360845 CGCATAGTTCCCTCGATTTC Chr9:121360806..121360825 59.67 50
downstream ENSMUSE00000507389 Chr9:121362326..121362562 GTTCATGGCTGAGGACTGGT Chr9:121362443..121362462 60.12 55
downstream ENSMUSE00000528159 Chr9:121363397..121363713 ACTCGGAGAAGCGTGAGTGT Chr9:121363638..121363657 60.06 55
downstream ENSMUSE00000633530 Chr9:121363397..121363862 ACTCGGAGAAGCGTGAGTGT Chr9:121363638..121363657 60.06 55
downstream ENSMUSE00000582958 Chr9:121369477..121369695 CTGAATTGGCGTGGAGGTAG Chr9:121369682..121369701 60.65 55
downstream ENSMUSE00000582957 Chr9:121378103..121378205 CGGCAAGTGGTAAAGGTGAA Chr9:121378166..121378185 61.05 50
downstream ENSMUSE00000582956 Chr9:121381355..121384034 CATGGTTGTCGTGGACTCAC Chr9:121381493..121381512 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCCTCCTCCTCTAAGATGC Chr9:121355039..121355059 60.17 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCCTCCTCCTCTAAGATGC Chr9:121355039..121355059 60.17 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032536